That's not exactly true. Nintendo has stated that they currently have no plans to release those titles. That doesn't mean that they won't get shuffled in a year or two from now. Once they made it past the Minish Caps, Golden Suns, Fire Emblems, Pokemons and Metroid Zero Missions, they'll realize that they still have Metroid Fusion, Mario Kart and Mario vs Donkey Kong, all great games that have already been converted to be compatible with the 3DS. Of course they will be made available eventually.
Cave Story is great, but be aware that it will get a 3D release later this year. It will cost more, but look a lot better.
As for the rest of the eshop games, I truly love Super Mario Land, Kirby's Dream Land and the Game Boy version of Donkey Kong. But I'll be honest, that might be my nostalgia goggles. I'd suggest watching the video trailers for those games before downloading them.
And then there's the DSi Ware versions of Earthworm Jim and Plants vs Zombies. Again, there's a DS module of Plants vs Zombies with more game modes, but at four times the cost of the download.
